Xie, Jing Ji, Tieming Ferreira, Marco A. R. Li, Yahan Patel, Bhaumik N. Rivera, Rocio M.
Published in
BMC Bioinformatics
BackgroundHigh-throughput sequencing experiments, which can determine allele origins, have been used to assess genome-wide allele-specific expression. Despite the amount of data generated from high-throughput experiments, statistical methods are often too simplistic to understand the complexity of gene expression. Specifically, existing methods do ...
Xu, Jing Wu, Peng Chen, Yuehui Meng, Qingfang Dawood, Hussain Dawood, Hassan
Published in
BMC Bioinformatics
BackgroundCancer subtype classification attains the great importance for accurate diagnosis and personalized treatment of cancer. Latest developments in high-throughput sequencing technologies have rapidly produced multi-omics data of the same cancer sample. Many computational methods have been proposed to classify cancer subtypes, however most of ...
Rogers, Alan R.
Published in
BMC Bioinformatics
BackgroundOur current understanding of archaic admixture in humans relies on statistical methods with large biases, whose magnitudes depend on the sizes and separation times of ancestral populations. To avoid these biases, it is necessary to estimate these parameters simultaneously with those describing admixture. Genetic estimates of population hi...
He, Hao Zhao, Jiaxiang Sun, Guiling
Published in
BMC Bioinformatics
BackgroundMolecular recognition features (MoRFs) are one important type of disordered segments that can promote specific protein-protein interactions. They are located within longer intrinsically disordered regions (IDRs), and undergo disorder-to-order transitions upon binding to their interaction partners. The functional importance of MoRFs and th...
Persson, Emma Kaduk, Mateusz Forslund, Sofia K. Sonnhammer, Erik L. L.
Published in
BMC Bioinformatics
BackgroundOrthology inference is normally based on full-length protein sequences. However, most proteins contain independently folding and recurring regions, domains. The domain architecture of a protein is vital for its function, and recombination events mean individual domains can have different evolutionary histories. It has previously been show...
Allendes Osorio, Rodolfo S. Tripathi, Lokesh P. Mizuguchi, Kenji
Published in
BMC Bioinformatics
BackgroundWhen visually comparing the results of hierarchical clustering, the differences in the arrangements of components are of special interest. However, in a biological setting, identifying such differences becomes less straightforward, as the changes in the dendrogram structure caused by permuting biological replicates, do not necessarily imp...
Jin, Huan Moseley, Hunter N. B.
Published in
BMC Bioinformatics
BackgroundStable isotope tracing can follow individual atoms through metabolic transformations through the detection of the incorporation of stable isotope within metabolites. This resulting data can be interpreted in terms related to metabolic flux. However, detection of a stable isotope in metabolites by mass spectrometry produces a profile of is...
Yang, Fan Liu, Yang Wang, Yanbin Yin, Zhijian Yang, Zhen
Published in
BMC Bioinformatics
BackgroundProtein subcellular localization plays a crucial role in understanding cell function. Proteins need to be in the right place at the right time, and combine with the corresponding molecules to fulfill their functions. Furthermore, prediction of protein subcellular location not only should be a guiding role in drug design and development du...
Kwon, Sunyoung Bae, Ho Jo, Jeonghee Yoon, Sungroh
Published in
BMC Bioinformatics
BackgroundQuantitative structure-activity relationship (QSAR) is a computational modeling method for revealing relationships between structural properties of chemical compounds and biological activities. QSAR modeling is essential for drug discovery, but it has many constraints. Ensemble-based machine learning approaches have been used to overcome ...
Ambler, Jon Mitchell Mulaudzi, Shandukani Mulder, Nicola
Published in
BMC Bioinformatics
BackgroundAs sequencing technology improves, the concept of a single reference genome is becoming increasingly restricting. In the case of Mycobacterium tuberculosis, one must often choose between using a genome that is closely related to the isolate, or one that is annotated in detail. One promising solution to this problem is through the graph ba...
